Bring r22915 from trunk to 1.8 branch:
Bring Coverity changes back to trunk:
r20399:
Change parse_command_line to free hand structure on error and only "leave()" at end of main.
r20400:
Purpose: Fix coverity issue 592
Description: Added void cast to call to H5F_sfile_assert_num() in
H5F_term)interface(). There is no need to check the return value of this
function in general, and there would be nothing to do even if it did fail.
r20401:
Added free(src_sizes) and free(src_offset). --gh
Tested on:
Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, threadsafe
(too minor for h5committest)
HDFFV-8012 - h5repack changes max dims and cause failure if only "-f none" is used without changing layout for chunked dataset when a chunk dim is bigger than a dataset dim
Description:
"h5repack -f <obj>:NONE <file.h5> out.h5" command failed if source file contains chunked dataset and a chunk dim is bigger than a dataset dim.
Another issue is that the command changed max dims if chunk dim is smaller than the dataset dim.
These issue occurred when dataset size is smaller than 64k (compact size limit)
Fixed them.
Merged from HDF5 trunk r22805
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
HDFFV-5919 - GMQS: h5diff - The number of object difference is not consistent between dataset and group/type when attribute(s) have differences
Description:
Object differences are not consistent between dataset and group/datatype when their attribute(s) have differences. This is because attribute(s) differences is not accumulated to group or datatype object’s difference, but accumulated to dataset difference.
To fix, do not accumulate attribute difference to dataset difference. This is referred to h5diff’s default behavior and also past report from users that users were confused by the accumulated behavior. (also can’t figure out only for dataset difference , also hard to spot dataset difference when it has lots of attributes or differences)
This also lead to fix inconsistent format indicating difference between dataset and group/datatype object.
Merged from HDF5 trunk r22751.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
Convert configure.in to configure.ac.
Align TESTS usage with autotools convention.
Update all references from configure.in to configure.ac
Tested: h5committest
Address HDFFV-7942 - h5diff: incorrect result for comparing attribute data with different type size in same class
Description:
When comparing attribute data values with same type class but different size, the result was incorrect. It was due to the size difference and got truncated.
Fixed to match up the smaller type size to big type size like what dataset does.
Merged from HDF5 trunk r22684 and r22691.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE cmake), cmake (jam)
Bring r22646 from trunk to 1.8 branch:
Changes resulting from Klocwork static analysis tool, from Mark Miller
@ LLNL (miller86@llnl.gov).
Tested on:
Mac OS X/64 10.7.4 (amazon) w/debug, C++ & FORTRAN, using gcc 4.7.x
(too minor to require h5committest)
HDFFV-8107 testh5diff will fail if build/test in HDF5 source tree
Description:
This is sub-task for "HDFFV-8105 testh5diff.sh uses the wrong operator (-a) in an if statement."
From the HDFFV-8105's update, h5diff test failed if build&test is performed in HDF5 source tree because 'cp' try to copy test files to self dir.
It's addressed by skipping if cp's src dir and dest dir is same.
Also this applied for all other tools under src/tools dir.
No change to the CMakeLists.txt files because CMake cautions/demands that in-source builds be avoided.
Merged from HDF5 trunk r22617.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), some manual tests as well
Purpose:
HDFFV-8003 - ph5diff (parallel h5diff): daily test failure on ember intermittently during non comparable test file comparison
HDFFV-7755 - parallel h5diff : hanging on koala intermittently during non comparable test file comparison
Description:
non-comparable test intermittently hung on koala and ember, but not on jam. it didn't occur until -np reaches 4 or bigger. it occurred once out of many repeated attempts of the same test.
There was a incorrectly (mistakenly?) duplicated code in MPI section which caused such hang in a certain condition. The test used more processes than other tests, which increased chance to trigger more undone processes, and such process could enter the incorrect code section and wait for wrong pair of send. it explains why it occurred intermittently according to machine condition and using a certain feature.
Removed incorrect code which blocked correct code.
Merged from HDF5 trunk r22618.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), some manually repeated test performed in parallel
Description:
The test command in COPY_TESTFILES_TO_TESTDIR used the wrong operator -a which
means and. It is not sufficient to test mere existence as $tstfile could have
been a directory or other non-file things. If the file is not readable, the
$CP command would fail but its return code was not checked.
Solution:
Get rid of the test command and go ahead to $CP it and then check its returned
code and report errors if detected.
Tested; committested.
(2) fix to extend into the aggregator based on threshold
(3) fix for the "flavor" logging problem
(4) fix for test failures due to the above fixes
(5) bug fix for h5stat when h5stat against a non-existing file
--Ths line, and th se below, will be ignored--
M test/mf.c
M src/H5MFaggr.c
M src/H5FDpublic.h
M src/H5MF.c
M src/H5FDmulti.c
M src/H5FDlog.c
M src/H5Faccum.c
M tools/h5copy/testfiles/h5copytst.out.ls
M tools/h5copy/testfiles/h5copy_ref.out.ls
M tools/h5stat/testh5stat.sh.in
M tools/h5stat/h5stat.c
HDFFV-7602 - GMQS: HDF5 command tools: Provide framework for reusable test files among tools
Stage2 working for h5diff tool.
Description:
Update cmake script to fetch test files from any tools to a test directory
and run test in organized manner.
Also keep the apperance similiar to shell script for better maintainance.
Tested:
CMake (Windows and jam)
Fix h5repacktst (test file generating binary) to address HDFFV-8016 h5repacktst failed in AIX 32bit mode
Description:
Segmentation fault occurred when h5repacktst try to generate a dataset when
system memory is limited to 256MB.
Add error handling to display apporiate message to exit and adjust the test
dataset according to the original size which didn't causing out of memory.
Tested: test was done by limit memory in csh.
jam (linux32-LE), ostrich (linuxppc64-BE)
The ph5diff (parallel h5diff) can intermittently hang in parallel mode
when comparing the two HDF5 files that contains common name objects with
different object types. (HDFFV-8003)
Skip only the specific test for parallel until the fix has made.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Fix for HDFFV-7998-h5diff: incorrect behavior and output for comparing symbolic dangling links without following-symlinks option
Description:
Fix not to check and display dangling link status without --follow-symlinks option.
Berfor the fix, when comparing symbolic link to symbolic link without follow-symlinks option, h5diff followed to check if those links are dangling or not. It caused to display output incorrectly (dangling link instead of symbolic link).
The fix also improved performance when comparing lots of symbolic links without the --follow-symlinks option.
Test cases were added and tagged with jira#.
This merged from HDF5 trunk r22319.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
Fix for HDFFV-8001 - h5unjam: segfault when used -V (show version) option
Description:
h5unjam has an option '-V' to display version information.
"h5unjam -V" caused segfulat for 1.8.9 pre-release.
Merged from HDF5 trunk 22300
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), Windows (32-LE cmake), Cmake (jam)
Bring r22287 from trunk to 1.8 branch:
Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward
the final design (as exemplified by the H5EA & H5FA code).
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
Fix for HDFFV-7993 - h5repack fails with error "chunk size must be <= maximum dimension size for fixed-sized dimensions"
Description:
Fixed a failure when change the chunk size of a specified chunked dataset with unlimited max dims.
Also took care of converting to contiguous and compact from the dataset.
Test cases were added and tagged with jira#.
Merged from HDF5 trunk r22277.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE cmake), Cmake (jam)
Bring r22180, r22181 and r22214 from trunk to 1.8 branch:
Add new "metadata block size" command line option ('-M <x>' or
'--metadata_block_size=<x>') for h5repack.
[With release managers blessing]
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug)
(h5committest upcoming)
Fix for HDFFV-7644 GMQS: h5diff - incorrect behaviors when comparing HDF5 files with different type of objects (dataset, group, type) as common objects
Description:
Fixed failure for comparing same named object with different object types in comparing groups. (common object comparison)
Prior to the fix, h5diff resulted in error. After the fix, h5diff detects such case as non-comparable and display messages accordingly.
Test cases were added and tagged with jira#.
Merged from HDF5 trunk 22176.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
update for HDFFV-7837 - h5diff: incorrect behavior with exclude-path option when unique object exist only in one file
Description:
Add the new test output list to test shell script.
This is based on the previous commit r22124.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE)
Fix for HDFFV-7837 - h5diff: incorrect behavior with exclude-path option when unique object exist only in one file
Description:
If unique objects exists only in one file and try to exclude
the unique objects with --exclude-path option, h5diff missed
excluding some objects.
Fixed to exclude objects correctly in such case.
Test cases were added and tagged with jira#.
Merged from HDF5 trunk r22114.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
